Contacts of the helix formed by residues 87 - 115 (chain B) in PDB entry 1JVM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 87 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA* 4.2 16.4 - - + +
85B THR* 2.8 7.2 + - - +
86B LEU* 1.3 81.8 - - + +
88B GLY* 1.3 58.3 + - - +
89B ARG 2.9 1.6 - - - -
90B CYS* 2.6 42.3 + - + +
91B VAL* 3.2 16.7 + - + +
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 5.1 3.3 - - - +
50B ALA* 4.2 7.3 - - - +
51B GLU* 4.0 7.4 - - - -
68B TRP* 4.3 2.9 - - - -
83B PRO* 3.4 19.4 - - - +
85B THR* 2.6 25.8 + - - -
87B TRP* 1.3 72.2 - - - +
89B ARG* 1.3 55.7 + - - +
91B VAL* 3.3 14.9 + - - +
92B ALA* 3.0 22.5 + - - +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO 4.9 3.4 + - - -
64A ARG* 5.0 5.3 + - - +
67A TRP* 2.8 73.4 - - + +
80A ASP* 4.4 7.7 + - - -
81A LEU* 5.0 2.4 - - - +
82B TYR* 4.9 1.8 - - - -
83B PRO* 3.0 41.3 + - + -
84B VAL* 3.5 24.1 + - - +
85B THR 3.0 16.8 - - - +
86B LEU* 4.0 9.6 - - - +
87B TRP 2.9 0.8 + - - -
88B GLY* 1.3 75.6 - - - +
90B CYS* 1.3 60.3 + - - +
92B ALA* 3.2 9.2 - - - +
93B VAL* 3.0 25.0 - - - +
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Residues in contact with CYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU 3.1 22.9 - - - -
87B TRP* 2.6 33.6 + - + +
89B ARG* 1.3 70.5 - - - +
91B VAL* 1.3 63.4 + - + +
92B ALA 2.8 5.3 + - - -
93B VAL* 3.1 9.2 + - - +
94B VAL* 3.1 29.7 + - + +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY* 3.4 26.9 - - - +
46B LEU* 4.0 27.6 - - + -
47B ALA* 3.4 36.6 - - + +
50B ALA* 4.7 4.7 - - + -
68B TRP* 4.4 4.3 - - + -
87B TRP* 3.6 16.6 - - + +
88B GLY* 3.5 11.2 - - - +
90B CYS* 1.3 76.7 - - + +
92B ALA* 1.3 59.9 + - - +
94B VAL* 3.6 7.8 + - - +
95B VAL* 2.9 29.6 + - - +
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 4.0 17.7 - - + -
78A TYR* 4.9 2.2 - - - +
68B TRP* 3.8 26.0 - - + -
83B PRO* 4.3 0.4 - - + -
88B GLY 3.0 12.8 + - - +
89B ARG* 3.2 16.6 - - - +
90B CYS 2.8 0.4 - - - -
91B VAL* 1.3 74.4 - - - +
93B VAL* 1.3 58.8 + - - +
95B VAL* 2.6 28.6 + - - +
96B MET* 2.9 21.5 + - + +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 4.9 2.0 - - + -
70A VAL* 3.9 25.8 - - + -
89B ARG 3.0 18.4 - - - +
90B CYS* 3.1 8.9 + - - +
92B ALA* 1.3 73.1 - - - +
94B VAL* 1.3 65.6 + - + +
96B MET* 3.2 14.3 - - + +
97B VAL* 2.9 43.1 + - + +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 4.1 17.9 - - + -
90B CYS* 3.1 15.7 + - + +
91B VAL* 3.7 10.8 - - - +
92B ALA 2.8 4.0 + - - -
93B VAL* 1.3 77.5 - - + +
95B VAL* 1.3 63.4 + - + +
97B VAL* 3.8 3.9 - - - +
98B ALA* 2.9 25.4 + - + +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 6.1 0.2 - - + -
39B VAL* 4.1 18.4 - - + +
40B LEU* 4.2 8.1 - - + -
43B GLY* 4.4 20.6 - - - -
68B TRP* 4.5 9.2 - - + -
69B SER* 3.6 31.6 - - - +
72B THR* 3.9 10.1 - - + -
73B ALA* 3.8 16.5 - - + +
91B VAL* 2.9 25.1 - - + +
92B ALA* 2.6 12.7 + - - +
94B VAL* 1.3 72.3 - - + +
96B MET* 1.3 65.7 + - - +
98B ALA* 3.1 4.0 - - - +
99B GLY 3.0 15.1 + - - -
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Residues in contact with MET 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 5.3 3.6 - - + -
70A VAL* 3.5 28.0 - - + -
71A GLU* 5.4 2.5 - - - -
74A THR* 3.7 24.7 - - + -
76A VAL* 3.4 28.3 - - + -
78A TYR* 5.2 4.0 - - - -
72B THR* 3.3 34.8 - - + +
73B ALA* 4.5 1.2 - - - +
75B THR* 5.3 0.2 - - + -
92B ALA* 2.9 12.1 + - + +
93B VAL* 3.2 30.5 - - + +
95B VAL* 1.3 74.5 - - - +
97B VAL* 1.3 66.8 + - - +
99B GLY* 2.8 5.7 + - - -
100B ILE* 2.8 30.3 + - + +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 5.5 2.2 - - + -
103A PHE* 4.1 24.0 - - + -
93B VAL* 2.9 32.0 + - + +
94B VAL* 4.0 3.4 - - - +
96B MET* 1.3 77.9 - - + +
98B ALA* 1.3 55.2 + - - +
100B ILE* 4.1 8.9 - - - +
101B THR* 2.4 49.4 + - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.5 16.8 - - + -
39B VAL* 3.9 22.9 - - + -
94B VAL* 2.9 16.3 + - + +
95B VAL 3.1 11.7 - - - +
96B MET 2.9 0.6 + - - -
97B VAL* 1.3 76.7 - - - +
99B GLY* 1.3 53.2 + - - +
101B THR* 3.3 4.4 - - - -
102B SER* 2.7 37.8 + - - +
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.3 22.5 - - - +
73B ALA* 3.5 17.7 - - - -
95B VAL 3.0 4.3 + - - -
96B MET 2.8 10.7 + - - -
98B ALA* 1.3 73.0 - - - +
100B ILE* 1.3 64.3 + - - -
102B SER 3.1 0.7 + - - -
103B PHE* 2.9 34.6 + - - -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 4.1 24.7 - - + +
103A PHE* 3.2 59.5 - - + -
107A THR* 5.2 1.6 + - - +
129A TBA 5.1 27.1 - - + -
73B ALA 4.0 2.5 + - - -
75B THR* 4.1 18.6 - - + -
96B MET* 2.8 32.3 + - + +
97B VAL 3.8 4.3 - - - +
99B GLY* 1.3 69.5 - - - +
101B THR* 1.3 53.3 + - - +
103B PHE* 4.0 3.4 - - - +
104B GLY* 2.8 32.2 + - - -
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 5.2 3.5 - - - -
106A VAL* 6.0 6.6 - - + +
110A LEU* 4.4 14.5 - - + +
97B VAL* 2.4 40.1 + - - +
98B ALA* 3.3 5.2 - - - -
100B ILE* 1.3 74.9 - - - +
102B SER* 1.3 58.3 + - - +
104B GLY* 3.1 2.4 + - - -
105B LEU* 2.8 35.3 + - + +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA* 3.9 27.2 + - - +
33B THR* 5.2 0.4 - - - -
35B LEU* 5.5 1.0 - - - +
36B LEU* 3.5 39.9 + - - +
98B ALA* 2.7 25.8 + - - -
99B GLY 3.1 0.6 + - - -
101B THR* 1.3 72.8 - - - +
103B PHE* 1.3 59.5 + - - +
105B LEU* 2.9 24.4 - - - +
106B VAL* 3.1 13.8 + - - +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TBA 6.0 4.7 - - + -
36B LEU* 4.2 19.1 - - + -
73B ALA* 4.0 16.8 - - + -
74B THR* 4.5 7.9 - - + -
99B GLY* 2.9 32.6 + - - +
100B ILE* 4.0 3.6 - - - +
102B SER* 1.3 69.6 - - - +
104B GLY* 1.3 68.1 + - - +
105B LEU 2.9 1.9 + - - -
106B VAL* 2.9 12.9 + - + +
107B THR* 2.8 27.4 + - - +
97C VAL* 3.9 29.6 - - + -
100C ILE* 3.1 56.8 - - + -
101C THR* 5.1 4.7 - - - -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.1 43.6 - - - +
110A LEU* 4.4 3.8 - - - -
100B ILE 2.8 18.0 + - - -
101B THR* 3.5 4.0 - - - -
103B PHE* 1.3 76.6 - - - +
105B LEU* 1.3 60.8 + - - +
107B THR* 3.4 5.2 - - - -
108B ALA* 3.2 11.8 + - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.7 30.5 - - + +
113A TRP* 5.6 1.8 - - + -
114A PHE* 4.0 26.9 - - + -
28B ALA* 3.5 21.5 - - + +
29B ALA* 3.7 13.7 - - + -
32B ALA* 3.4 30.3 - - + -
101B THR* 2.8 13.7 + - + +
102B SER* 2.9 12.6 - - - +
104B GLY* 1.3 73.1 - - - +
106B VAL* 1.3 57.0 + - + +
107B THR 3.0 1.3 - - - -
108B ALA* 2.6 31.8 + - - +
109B ALA* 2.9 6.0 + - + +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 4.8 17.3 - - + +
32B ALA* 5.2 2.0 - - + -
33B THR* 5.6 4.0 - - - +
102B SER* 3.5 14.4 - - - +
103B PHE* 2.9 13.2 + - + +
105B LEU* 1.3 85.2 - - + +
107B THR* 1.3 60.8 + - - +
109B ALA* 3.8 9.4 - - + +
110B LEU* 3.1 32.6 + - + +
101C THR* 5.7 10.1 - - + +
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 4.3 11.0 - - + -
103B PHE* 2.8 17.6 + - - +
104B GLY* 3.4 13.8 - - - -
106B VAL* 1.3 76.9 - - - +
108B ALA* 1.3 63.0 + - - +
110B LEU* 3.5 6.5 + - - +
111B ALA* 3.2 21.9 + - + +
100C ILE* 5.1 0.9 + - - +
104C GLY* 2.8 46.0 - - - +
107C THR* 4.1 17.5 - - + -
108C ALA* 4.0 3.4 - - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 4.3 3.1 - - - +
110A LEU* 4.2 5.4 - - + -
111A ALA* 3.6 38.4 - - + +
114A PHE* 4.1 10.5 - - + -
104B GLY 3.2 11.8 + - - +
105B LEU* 2.6 23.7 + - - +
107B THR* 1.3 69.7 - - - +
109B ALA* 1.3 58.4 + - - +
111B ALA* 3.1 4.2 + - - +
112B THR* 2.8 32.6 + - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 4.0 8.2 - - + -
25B HIS* 3.7 22.6 + - + +
26B TRP* 4.5 13.9 - - + -
29B ALA* 5.0 10.8 - - + -
105B LEU* 2.9 10.5 + - + +
106B VAL* 3.9 11.9 - - + +
107B THR 3.4 0.2 - - - -
108B ALA* 1.3 76.4 - - - +
110B LEU* 1.3 63.9 + - - +
112B THR* 3.1 12.3 - - - +
113B TRP* 3.1 26.4 + - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TRP* 5.2 8.0 - - + -
106B VAL* 3.1 27.7 + - + +
107B THR* 3.6 6.3 - - - +
109B ALA* 1.3 76.4 - - - +
111B ALA* 1.3 60.0 + - - +
113B TRP* 3.4 33.6 - - + -
114B PHE* 3.3 20.6 + - - -
101C THR* 4.2 16.8 - - + +
104C GLY 4.4 2.2 - - - -
105C LEU* 3.5 52.9 - - + +
108C ALA* 4.0 8.5 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 5.3 6.5 - - + -
107B THR* 3.2 6.4 + - + +
108B ALA* 3.1 9.1 + - - +
110B LEU* 1.3 76.6 - - - +
112B THR* 1.3 57.0 + - - +
113B TRP 2.9 4.7 - - - -
114B PHE* 2.6 29.7 + - - +
115B VAL* 3.1 14.6 + - + +
108C ALA* 3.3 35.2 - - + +
111C ALA* 5.2 6.5 - - + -
112C THR* 4.2 2.0 + - - +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 4.6 2.6 - - - +
114A PHE* 3.3 39.8 + - + +
115A VAL* 3.5 20.1 - - - +
118A GLU* 4.4 8.1 - - - +
25B HIS* 3.1 42.5 - - + +
108B ALA 2.8 19.8 + - - +
109B ALA* 3.1 10.8 - - - +
111B ALA* 1.3 71.3 - - - +
113B TRP* 1.3 57.8 + - - +
115B VAL* 3.7 7.0 + - - +
116B GLY* 3.5 13.5 + - - -
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B HIS* 4.2 7.2 - + - +
26B TRP* 3.5 35.1 - + + -
109B ALA 3.1 19.2 + - - +
110B LEU* 3.4 37.0 - - + +
112B THR* 1.3 77.9 - - - +
114B PHE* 1.3 83.7 + + - +
115B VAL 3.2 0.4 - - - -
116B GLY* 2.7 26.4 + - - -
117B ARG* 3.4 9.6 + - + +
28C ALA* 5.4 4.3 - - + -
105C LEU* 5.4 1.3 - - + -
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU 3.3 11.9 + - - -
111B ALA 2.6 16.6 + - - +
113B TRP* 1.3 100.3 - + - +
115B VAL* 1.3 53.5 + - - +
116B GLY 3.0 4.9 - - - -
117B ARG* 3.4 7.1 + - + +
118B GLU* 3.2 24.9 + - - +
25C HIS* 3.3 38.2 + + + +
28C ALA* 3.3 29.8 - - + -
105C LEU* 4.0 20.9 - - + -
108C ALA* 4.2 4.9 - - + -
109C ALA* 3.9 22.4 - - + -
112C THR* 3.3 29.7 + - + +
----------------------------------------------------------
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 4.6 25.6 - - + -
119A GLN* 5.1 1.7 - - - +
111B ALA 3.1 10.6 + - - +
112B THR* 4.0 11.7 - - - +
113B TRP 3.2 0.4 - - - -
114B PHE* 1.3 74.3 - - - +
116B GLY* 1.3 60.1 + - - +
117B ARG 3.4 0.2 - - - -
118B GLU* 3.7 10.1 - - + -
119B GLN* 3.4 36.7 + - + +
112C THR* 3.0 35.4 - - - +
115C VAL* 4.6 21.3 - - + -
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il